Search

The South China tigers (Panthera tigris amoyensis) are extinct in the wild, but viable populations remain in breeding centers and zoos after 60 years of effective conservation efforts. At present, however, the existing genetic variation of these tigers remains unknown. In this study, we assembled a high-quality chromosome-level genome using long-read sequences and re-sequenced 29 high-depth genomes of the South China tigers. We identified two significantly differentiated genomic ancestries in the extant populations, which also harbored some rare genetic variants introgressed from other subspecies, suggesting limited but essential genetic diversity to sustain the South China tigers. The unique pattern of dual ancestry and the genomic resources generated in our study pay the way for a genomics-informed conservation, following the real-time monitoring and controlled exchange of all reproductive South China tigers.

Gut microbiota influences nutrient metabolism and immunity of animal hosts. Better understanding of the composition and diversity of gut microbiota contributes to conservation and management of threatened animals both in situ and ex situ. In this study, we applied 16S rRNA gene amplicon sequencing to evaluate the composition and diversity of the fecal bacterial community of four gibbon genera (Family Hylobatidae) at four Chinese zoos. The results showed that the dominant bacterial phyla were Bacteroidetes, Firmicutes, and Proteobacteria and dominant families were Prevotellaceae (Bacteroidetes), Spirochaetaceae (Spirochaetes) and Ruminococcaceae (Firmicutes) in the gut of all gibbons. Both captive site and host genus had significant effects on the relative abundance of dominant bacteria and structure of gut bacterial community. We found that captive site and host genus did not solely impact gut bacterial diversity, but the interaction between them did. This study provides basic knowledge for gut microbiota of all four gibbon genera and contributes to management and conservation of captive gibbons.

Microarrays can be a cost-effective alternative to high-throughput sequencing for discovering novel single-nucleotide polymorphisms (SNPs). Illumina’s iScan platform dominates the market, but their commercial microarray products are designed for model organisms. Further, the platform outputs data in a proprietary format. This cannot be easily converted to human-readable genotypes or be merged with pre-existing data. To address this, we present and validate a novel pipeline to facilitate data analysis from cross-species application of Illumina microarrays. This facilitates the generation of a compatible VCF from iScan data and the merging of this with a second VCF comprising genotypes derived from other samples and sources. Our pipeline includes a custom script, iScanVCFMerge (presented as a Python package), which we validate using iScan data from three great ape genera. We conclude that cross-species application of microarrays can be a rapid, cost-effective approach for SNP discovery in non-model organisms. Our pipeline surmounts the common challenges of integrating iScan genotypes with pre-existing data.

We monitored the reproductive parameters of South China Tigers (SCT) in captivity from 1983 to 2018. Tigers gave birth in all but 3 months of the year, with a peak in May, June, and July (goodness of fit test, χ2 = 49.928, p = 0.000, n = 270 litters from 65 mothers). The minimum age at 1st reproduction was 4.96 ± 2.43 (standard deviation, SD) years. The mean interval between litters was 410.2 ± 290.2 (SD) days (n = 38 pairs with consecutive reproduction). Mean litter size was 2.1 ± 0.9 (SD) (n = 270 litters from 65 tigers). The average survival rate of newborn cubs was 55.7% (SD = 17.7). There was significant maternal age variation among the litters studied. Reproduction mainly occurs in females in their prime (3–14 years old), with little in young and old females (one-way analysis of variance, ANOVA, F = 8.314, p = 0.005). Reproductive parameters of SCTs could be the basis of analysis on the population dynamics and management, and genetic considerations are necessary to plan future breeding programs and to assist in the selection of individuals for reintroduction to the wild.

Based on “Presence data”, we assessed the habitat quality according to the physical factor utilized by Tibetan fox in Gouli Township, Dulan County, Qinghai Province, China. The spatial carrying capacity of Tibetan fox was also estimated according to their minimum space requirements. A total of 4 topographical factors, elevation, slope, terrain ruggedness and slope position, were used to conduct habitat assessment for Tibetan fox. The suitability of habitat factors were determined by comparing the utilization by Tibetan fox and its availability based on 95% Bonferroni confidence interval. A comprehensive assessment criterion was set up for all topographic factors. For Tibetan fox, the elevations of 4 050 - 4 300 m, the slopes of 5 − 20°, the upper and lower slope positions were suitable habitat. Tibetan fox use terrain ruggedness non-selectively. According to the utilization of Tibetan fox on different topographic factors and the consistence of habitat utilization by different fox individuals, we set the comprehensive criterion as: Xi = (X2elevation x X2slope positionx Xslope x Xterrainrug gadness)1/6. The area of suitable habitat is about 17.4 km2, which take a percentage of 38.8% of research area. The area of most suitable habitat is only 0.4 km2. The home range of Tibetan fox ranges from 2.53 km2 to 4.99 km2, and the overlap index (OI) of different individuals were 0.16 − 0.66. The minimum space requirements of Tibetan fox are 2.09 − 3.55 km2, and the spatial carrying capacity of Tibetan fox in suitable habitat is 7−12. According to the habitat resource and monitoring results, we infer that the Tibetan fox population is keeping steady.